Setup

Load R libraries

library(data.table)
library(ggplot2)
library(ggpubr)
library(tidyr)
library(limma)
library(biomaRt)
library(fgsea)
library(goseq)

theme_set(theme_classic())

cell_type_name = params$cell_type_name
graph_weight = params$graph_weight

cell_type_name
## [1] "cd4"
graph_weight
## [1] "5.0"

Check enrichment of gene sets

Read in gene info and gene set assignments

file_tag = sprintf("%s_BL_%s", cell_type_name, graph_weight)

assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag), 
                     what = character(), sep="\n")

gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag), 
                 what = character(), sep="\n")

gene_sets = sapply(gene_sets, strsplit, USE.NAMES=FALSE, split=",")
n_genes   = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##     4.0    23.0    24.0    23.3    25.0    26.0
length(n_genes)
## [1] 40
sort(n_genes)
##  [1]  4 19 20 22 22 22 22 22 23 23 23 23 23 23 24 24 24 24 24 24 24 24 24 24 25
## [26] 25 25 25 25 25 25 25 25 25 25 25 25 25 25 26

Find gene symbols

Find gene symbols from bioMart.

All the gene symbols that can be found in bioMart are consistent with what we have. So no need to run it.

ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")

gene_BM = getBM(attributes = c("hgnc_symbol", "external_gene_name"), 
                filters = "external_gene_name", 
                values = assayed_genes, 
                mart = ensembl)
length(assayed_genes)
dim(gene_BM)
gene_BM[1:2,]

table(assayed_genes %in% gene_BM$external_gene_name)

t1 = table(gene_BM$external_gene_name)
dup = names(t1)[t1 > 1]
gene_BM[gene_BM$external_gene_name %in% dup,]

table(gene_BM$hgnc_symbol == gene_BM$external_gene_name)
w2kp = which(gene_BM$hgnc_symbol != gene_BM$external_gene_name)
gene_BM[w2kp,]

Find gene symbols using the alias2Symbol function from limma.

a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
  gi = assayed_genes[i]
  ai = alias2Symbol(gi)
  if(length(ai) > 1){
    print(gi)
    print(ai)
  }
  a2s[i] = ai[1]
}
## [1] "HIST1H2BC"
## [1] "H2BC5" "H2BC4"
## [1] "MPP6"
## [1] "MPHOSPH6" "PALS2"   
## [1] "MARS"
## [1] "MARS1" "SLA2" 
## [1] "SEPT2"
## [1] "SEPTIN6" "SEPTIN2"
table(is.na(a2s))
## 
## FALSE  TRUE 
##  1951    49
table(a2s == assayed_genes, useNA = 'ifany')
## 
## FALSE  TRUE  <NA> 
##    45  1906    49
gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)

gene_info[sym_in_data != sym_limma,]
##      sym_in_data   sym_limma
##  1:      ADPRHL2       ADPRS
##  2:          AES        TLE5
##  3:     C12orf45    NOPCHAP1
##  4:      C3orf58      DIPK2A
##  5:      C6orf99   LINC02901
##  6:        CBWD2       ZNG1B
##  7:      CXorf57        RADX
##  8:      FAM102A       EEIG1
##  9:      FAM122C      PABIR3
## 10:      FAM153C    FAM153CP
## 11:     FAM160A2      FHIP1B
## 12:        GRASP     TAMALIN
## 13:        H2AFX        H2AX
## 14:    HIST1H2AG      H2AC11
## 15:    HIST1H2BC       H2BC5
## 16:    HIST1H2BK      H2BC12
## 17:    HIST1H2BN      H2BC15
## 18:     HIST1H3A        H3C1
## 19:     HIST1H3H       H3C10
## 20:     HIST1H4C        H4C3
## 21:    HIST2H2BF      H2BC18
## 22:         LRMP       IRAG2
## 23:      MFSD14C    MFSD14CP
## 24:         MKL1       MRTFA
## 25:         MPP6    MPHOSPH6
## 26:  RNASEH1-AS1  RNASEH1-DT
## 27:        SEPT6     SEPTIN6
## 28:        SEPT9     SEPTIN9
## 29: TMEM161B-AS1 TMEM161B-DT
## 30:        ARNTL       BMAL1
## 31:     C6orf106       ILRUN
## 32:     C6orf203      MTRES1
## 33:      FAM129A      NIBAN1
## 34:     FAM160B1      FHIP2A
## 35:      FAM192A    PSME3IP1
## 36:        HEXDC        HEXD
## 37:     HIST1H1E        H1-4
## 38:     KIAA0100       BLTP2
## 39:     KIAA1551       RESF1
## 40:         LARS       LARS1
## 41:         MARS       MARS1
## 42:      PLA2G16      PLAAT3
## 43:        SEPT2     SEPTIN6
## 44:       SMIM37        MTLN
## 45:         YARS       YARS1
##      sym_in_data   sym_limma
gene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma), gene_symbol := sym_limma]

dim(gene_info)
## [1] 2000    3
gene_info[1:5,]
##    sym_in_data sym_limma gene_symbol
## 1:       ABCD3     ABCD3       ABCD3
## 2:       ABCG1     ABCG1       ABCG1
## 3:       ABHD5     ABHD5       ABHD5
## 4:        ABI1      ABI1        ABI1
## 5:      ABLIM1    ABLIM1      ABLIM1
t1 = table(gene_info$gene_symbol)
table(t1)
## t1
##    1    2 
## 1998    1
gene_info[gene_symbol %in% names(t1)[t1 == 2],]
##    sym_in_data sym_limma gene_symbol
## 1:       SEPT6   SEPTIN6     SEPTIN6
## 2:       SEPT2   SEPTIN6     SEPTIN6
gene_info[sym_in_data == "HIST1H2BC", gene_symbol:="H2BC4"]
gene_info[sym_in_data == "SEPT6", gene_symbol:="SEPTIN6"]
gene_info[sym_in_data == "SEPT2", gene_symbol:="SEPTIN2"]

Prepare gene set information

Gene set annotations (by gene symbols) were downloaded from MSigDB website.

gmtfile = list()
gmtfile[["reactome"]] = "../Annotation/c2.cp.reactome.v2023.2.Hs.symbols.gmt"
gmtfile[["go_bp"]]    = "../Annotation/c5.go.bp.v2023.2.Hs.symbols.gmt"
gmtfile[["immune"]]   = "../Annotation/c7.all.v2023.2.Hs.symbols.gmt"

pathways = list()
for(k1 in names(gmtfile)){
  pathways[[k1]] = gmtPathways(gmtfile[[k1]])
}

names(pathways)
## [1] "reactome" "go_bp"    "immune"
sapply(pathways, length)
## reactome    go_bp   immune 
##     1692     7647     5219

Filter gene sets for size between 10 and 500.

lapply(pathways, function(v){
  quantile(sapply(v, length), probs = seq(0, 1, 0.1), na.rm = TRUE)
})
## $reactome
##     0%    10%    20%    30%    40%    50%    60%    70%    80%    90%   100% 
##    5.0    7.0    9.0   12.0   17.0   23.0   31.0   44.0   71.8  120.9 1463.0 
## 
## $go_bp
##     0%    10%    20%    30%    40%    50%    60%    70%    80%    90%   100% 
##    5.0    6.0    8.0   10.0   14.0   19.0   29.0   46.0   80.8  183.0 1966.0 
## 
## $immune
##   0%  10%  20%  30%  40%  50%  60%  70%  80%  90% 100% 
##    5  162  193  197  199  199  200  200  200  200 1992
for(k1 in names(pathways)){
  p1 = pathways[[k1]]
  pathways[[k1]] = p1[sapply(p1, length) %in% 10:500]
}

Conduct enrichment analysis

dim(gene_info)
## [1] 2000    3
max_n2kp = 10

goseq_res = NULL

for(k in 1:length(gene_sets)){
  if(length(gene_sets[[k]]) < 10) { next }
  
  print(k)
  set_k = paste0("set_", k)
  print(gene_sets[[k]])
  
  genes = gene_info$sym_in_data %in% gene_sets[[k]]
  names(genes) = gene_info$gene_symbol
  table(genes)
  
  pwf = nullp(genes, "hg38", "geneSymbol")

  for(k1 in names(pathways)){
    p1 = pathways[[k1]]
    res1 = goseq(pwf, "hg38", "geneSymbol", 
                 gene2cat=goseq:::reversemapping(p1))
    res1$FDR  = p.adjust(res1$over_represented_pvalue, method="BH")
    
    nD = sum(res1$FDR < 0.1)
    
    if(nD > 0){
      res1 = res1[order(res1$FDR),][1:min(nD, max_n2kp),]
      res1$category = gsub("REACTOME_|GOBP_", "", res1$category)
      res1$category = gsub("_", " ", res1$category)
      res1$category = tolower(res1$category)
      res1$category = substr(res1$category, start=1, stop=81)
      goseq_res[[set_k]][[k1]] = res1
    }
  }
}
## [1] 1
##  [1] "ADK"      "KIF9"     "SNHG7"    "UPF3A"    "AP3M2"    "APBB1IP" 
##  [7] "ATXN7L3B" "BROX"     "C2orf68"  "CYTIP"    "ENY2"     "IFITM2"  
## [13] "IRAK4"    "PKNOX1"   "PLAC8"    "PRMT2"    "SDR39U1"  "SEC14L1" 
## [19] "SESN3"    "SETD5"    "SIGIRR"   "STK17B"

## [1] 2
##  [1] "CCM2"     "CHURC1"   "DNAAF2"   "EVI2B"    "FCER1G"   "LEPROTL1"
##  [7] "NMT2"     "PTGER4"   "RNF220"   "SCPEP1"   "SERTAD1"  "SFI1"    
## [13] "SNX18"    "TMEM107"  "TNFRSF25" "APOBEC3G" "EMP3"     "FAM53B"  
## [19] "KLRG1"    "LAG3"     "SCAMP4"   "SPOCK2"   "UBR2"

## [1] 3
##  [1] "AC008105.3"   "AC093323.1"   "AK5"          "AL359220.1"   "ARRDC2"      
##  [6] "BOLA2-SMG1P6" "COQ8A"        "GPCPD1"       "IGLV1-44"     "JCHAIN"      
## [11] "LINC01215"    "LRMP"         "LST1"         "MDS2"         "MFSD14C"     
## [16] "MUC20-OT1"    "NAA16"        "PLCL1"        "SPART"        "TMEM161B-AS1"
## [21] "TRAV38-2DV8"  "TRBV7-3"      "ZNF600"       "ZNF749"       "ZNF862"

## [1] 5
##  [1] "AC007952.4" "AC013264.1" "AC025171.2" "AC087239.1" "AC245014.3"
##  [6] "AL138963.3" "ANXA2R"     "DELE1"      "IGKV3-20"   "JAML"      
## [11] "LRRC8C-DT"  "LRRN3"      "NR4A2"      "SCML4"      "SNHG8"     
## [16] "ST7L"       "TBCC"       "TMEM71"     "TRAV8-6"    "TRBV28"    
## [21] "TRBV5-4"    "WASHC4"     "ZFP14"      "ZNF506"     "MATK"

## [1] 6
##  [1] "AC145124.1"  "ARHGAP15"    "C12orf29"    "COX10"       "CST3"       
##  [6] "DPYD"        "ERAP2"       "IGLV2-14"    "KCNK6"       "TOMM7"      
## [11] "TRAV12-2"    "TRAV13-2"    "TRAV21"      "TRAV41"      "TRBC1"      
## [16] "TRBC2"       "TRBV6-2"     "TRBV6-6"     "TSPOAP1-AS1" "TTC39C"     
## [21] "UCP2"        "CCL5"        "CCR4"        "FRMD4B"      "GZMA"

## [1] 7
##  [1] "AC009061.2" "AMD1"       "CD96"       "COA1"       "HELQ"      
##  [6] "LDLRAP1"    "RNASEK"     "ARID5B"     "CARD11"     "CCDC112"   
## [11] "CHD6"       "COX17"      "CRTC3"      "ERICH1"     "GON4L"     
## [16] "KIAA1551"   "KIF3B"      "MIER1"      "NADSYN1"    "NBEAL2"    
## [21] "SLC23A2"    "STK10"      "TCF25"      "TRAC"       "ZNF267"

## [1] 8
##  [1] "ANAPC4"   "BTG1"     "BTG2"     "CHD2"     "EIF1"     "EPHB6"   
##  [7] "FBXL3"    "LYRM7"    "PHC1"     "PLK2"     "PNRC1"    "PPIL3"   
## [13] "SFMBT1"   "ZFP36L1"  "CCDC12"   "CGGBP1"   "DPP7"     "GPHN"    
## [19] "PCGF5"    "PUS7L"    "SMAP1"    "SREK1IP1"

## [1] 9
##  [1] "ABHD5"     "ATG13"     "CD38"      "FCGR3A"    "LAX1"      "MMP24OS"  
##  [7] "ODF2L"     "PNPLA2"    "RASA2"     "RCSD1"     "SNRK"      "TESPA1"   
## [13] "TMC8"      "TRAV23DV6" "TRAV8-2"   "TUBD1"     "TUBE1"     "ZBTB25"   
## [19] "HSH2D"     "IFI44"     "IFI44L"    "OAS1"      "TRAT1"

## [1] 10
##  [1] "ABCC10"     "ABHD3"      "AC116407.2" "AC118549.1" "ADTRP"     
##  [6] "C20orf204"  "CARMIL2"    "CFD"        "FAAH2"      "GPR132"    
## [11] "HRH2"       "LRRC58"     "MIAT"       "NORAD"      "NRDC"      
## [16] "OSM"        "PCSK1N"     "SLF2"       "SLFN12L"    "SPATA13"   
## [21] "TOMM70"     "TRANK1"     "UBALD2"     "Z93930.2"   "ZFYVE28"

## [1] 11
##  [1] "BDH1"     "CCR6"     "CD48"     "LCLAT1"   "PTPRCAP"  "RNF139"  
##  [7] "SLC12A6"  "SLC25A25" "TRAM1"    "ATP8B2"   "CD2"      "CD58"    
## [13] "CMTM6"    "GIMAP4"   "HM13"     "LPCAT3"   "LPCAT4"   "LPGAT1"  
## [19] "SLC12A9"

## [1] 12
##  [1] "AC119396.1" "AF213884.3" "AL118516.1" "AL627171.1" "AL645728.1"
##  [6] "C12orf57"   "C6orf99"    "CHRM3-AS2"  "CSKMT"      "EGR1"      
## [11] "HIPK1-AS1"  "HIST1H2BC"  "ILF3-DT"    "LINC00649"  "LINC01550" 
## [16] "METTL21A"   "MID1IP1"    "NPIPB11"    "NUP58"      "ORC4"      
## [21] "TC2N"       "TMEM154"    "TRABD2A"    "TMEM175"

## [1] 13
##  [1] "AKT3"     "C12orf45" "C1orf43"  "EPHX2"    "GTPBP6"   "IP6K2"   
##  [7] "LBH"      "NR1D1"    "NR1D2"    "PAPOLG"   "PDCD7"    "PDE3B"   
## [13] "PHLDA1"   "PPP1R15B" "TMEM63A"  "TNFAIP8"  "TTC3"     "DHX29"   
## [19] "EAPP"     "EHMT1"    "POGLUT1"  "SPTLC2"   "TCIRG1"

## [1] 14
##  [1] "ACADSB"    "ACSS1"     "ANKH"      "ARID4A"    "ARMH1"     "C7orf31"  
##  [7] "CAMK4"     "CFAP36"    "CTSF"      "DAPP1"     "FAM153C"   "FCMR"     
## [13] "FOSB"      "FYB1"      "HIST1H4C"  "IER2"      "IFRD1"     "ING2"     
## [19] "MTRNR2L12" "MXD1"      "PLEKHM1"   "RGCC"      "TGIF1"     "YY1AP1"

## [1] 15
##  [1] "CHIC2"      "DHRS3"      "ADGRE5"     "AKNA"       "C12orf75"  
##  [6] "CARD16"     "CD69"       "GRK2"       "KANSL1-AS1" "KIAA0040"  
## [11] "MT1X"       "MTRNR2L8"   "NAA38"      "NBDY"       "NDUFC1"    
## [16] "NSD3"       "PAXX"       "PTGER2"     "PUM3"       "RASAL3"    
## [21] "TRAV29DV5"  "TRBV12-3"   "TSPAN32"    "TUT4"       "USP30-AS1"

## [1] 16
##  [1] "AC015982.1" "AC027644.3" "AC084033.3" "AC097376.2" "AL135791.1"
##  [6] "ARF4-AS1"   "ARL4A"      "CERNA1"     "CHMP7"      "FAM102A"   
## [11] "FAM122C"    "GOLGA8B"    "IL23A"      "LETM2"      "LINC02265" 
## [16] "LINC02273"  "NDUFV2-AS1" "NOCT"       "NPIPB5"     "NSMCE3"    
## [21] "PRR7"       "RGS1"       "THAP9-AS1"  "ATAD2B"     "NUP160"

## [1] 17
##  [1] "AKIRIN1" "AKIRIN2" "GIMAP8"  "OSER1"   "PCMTD2"  "PYROXD1" "RABL2B" 
##  [8] "STMN3"   "TECPR1"  "ZFX"     "ZNF140"  "CAMTA2"  "DOCK11"  "NDUFA3" 
## [15] "NRROS"   "OAS2"    "PPP2R3C" "PSMB9"   "RNF19A"  "SRP54"   "TBC1D14"
## [22] "TRAPPC8" "UBA7"    "UTP25"

## [1] 18
##  [1] "CD28"    "DBP"     "PECAM1"  "BATF"    "CD320"   "CISH"    "CMIP"   
##  [8] "FBXO9"   "G2E3"    "IFI35"   "IL2RB"   "IL2RG"   "IL32"    "INPP5D" 
## [15] "MYOM2"   "NQO2"    "P4HTM"   "RAPGEF1" "SLC35A2" "TIPARP"  "UGCG"   
## [22] "ZNF276"  "ZNF708"

## [1] 19
##  [1] "AC025159.1" "AC087623.3" "COQ7"       "EFCAB2"     "ENOSF1"    
##  [6] "FOXN3"      "GADD45B"    "GRASP"      "KCNQ1OT1"   "MBD6"      
## [11] "NSUN6"      "ODC1"       "SLC22A17"   "SNHG12"     "TBCCD1"    
## [16] "TCTA"       "YPEL2"      "AC022916.1" "ANKAR"      "AREG"      
## [21] "ITK"        "SNHG9"      "TAF4B"      "TNFRSF4"    "UBE3B"

## [1] 20
##  [1] "C16orf74" "C3orf58"  "CCDC141"  "CCDC66"   "CEP95"    "CHMP1B"  
##  [7] "FAM117B"  "IL6R"     "MAST4"    "PHYH"     "PIK3IP1"  "PNISR"   
## [13] "RCAN3"    "RIC1"     "SH3YL1"   "SLC44A1"  "STX16"    "TBCK"    
## [19] "TSC22D2"  "WARS2"    "ADAM19"   "C12orf4"  "HELB"     "WDR7"

## [1] 21
##  [1] "ADPRHL2"    "BTN3A1"     "LTA4H"      "PITPNA-AS1" "TMEM245"   
##  [6] "UTP6"       "ALOX5AP"    "APOL1"      "APOL6"      "BTN3A2"    
## [11] "BUD23"      "CTSW"       "ECPAS"      "GBP1"       "GBP3"      
## [16] "GBP5"       "GZMM"       "HEXDC"      "MCTP2"      "NCBP3"     
## [21] "PEX11B"     "SP140"      "TAOK3"      "TGFBR3"     "TMEM62"

## [1] 22
##  [1] "RBKS"     "ZSCAN18"  "ABHD2"    "APH1B"    "CITED4"   "DDX3Y"   
##  [7] "EIF1AY"   "GABPB2"   "IL21R"    "KDM5D"    "KHNYN"    "KIF21B"  
## [13] "RNF157"   "RPS4Y1"   "RTKN2"    "SBNO2"    "SLC25A37" "SUSD6"   
## [19] "TENT5C"   "TMEM156"  "TTTY15"   "UTY"

## [1] 23
##  [1] "ASAH1"   "HVCN1"   "MYADM"   "OXLD1"   "AGAP2"   "ARHGAP4" "BLOC1S6"
##  [8] "CD55"    "CD7"     "DIP2A"   "GGCX"    "IFNAR1"  "IFNGR2"  "MORC3"  
## [15] "NME3"    "NPDC1"   "PIEZO1"  "PSME2"   "REXO2"   "SCAF8"   "TIMP1"  
## [22] "UQCC2"   "ZDHHC20"

## [1] 24
##  [1] "COL18A1"   "DALRD3"    "NECAP2"    "ADGRG1"    "ARHGEF3"   "ARL4C"    
##  [7] "COL6A3"    "COLGALT1"  "CX3CR1"    "FGFBP2"    "LAIR2"     "LINC01871"
## [13] "LPIN1"     "LPIN2"     "LY96"      "PCED1B"    "PLEK"      "RAP1GAP2" 
## [19] "RNPEPL1"   "SP140L"    "TCAF2"     "TTC16"     "VPS13D"    "ZNF683"

## [1] 25
##  [1] "C6orf62" "CCNH"    "COQ10B"  "DGKA"    "ERCC5"   "FHIT"    "INPP4B" 
##  [8] "KLHL24"  "LEF1"    "MYNN"    "NFYB"    "TCF7"    "TPP2"    "ACAP1"  
## [15] "CREBZF"  "ETNK1"   "NARF"    "NFE2L1"  "PPRC1"   "RHOH"    "STAT4"  
## [22] "TGS1"    "VPS36"   "XBP1"

## [1] 26
##  [1] "AP002360.1" "ATG9B"      "CITED2"     "FBXO3"      "KIAA1328"  
##  [6] "MAML2"      "MBNL2"      "MHENCR"     "MLXIP"      "MMP28"     
## [11] "MTERF4"     "PDE7A"      "PLCD1"      "RAB33B"     "RETREG1"   
## [16] "SLC8B1"     "TAGAP"      "THAP6"      "TRAV8-3"    "TSPYL4"    
## [21] "WHAMM"      "WSB1"       "XIST"       "ZNF10"      "CCDC43"

## [1] 27
##  [1] "CBR3"     "DPEP2"    "GGT7"     "LIMS1"    "NEU1"     "SERTAD2" 
##  [7] "SLC25A32" "USP3"     "ZNF677"   "B3GALT4"  "FKBP11"   "FUT11"   
## [13] "GALNS"    "GZMB"     "PARVG"    "PLAA"     "RSU1"     "SACS"    
## [19] "SH3BGRL3" "SRGN"     "ST6GAL1"  "TRIB2"

## [1] 28
##  [1] "MZF1"    "NSMAF"   "YPEL5"   "C4orf48" "CROT"    "DENND4B" "EFR3A"  
##  [8] "EIF2AK4" "GNLY"    "ISG20"   "KCNAB2"  "KLF9"    "KLHDC4"  "LTBP4"  
## [15] "NEK9"    "NLRC5"   "NT5C"    "PDE4B"   "PREP"    "PREX1"   "PTPRE"  
## [22] "RCBTB2"  "SYTL1"   "ZNF236"  "ZNF292"

## [1] 29
##  [1] "ABCG1"       "AIF1"        "ARHGAP9"     "CD40LG"      "CRLF3"      
##  [6] "DNASE1"      "GIMAP1"      "HIST1H3H"    "IPCEF1"      "JPX"        
## [11] "KLF7"        "LIPT1"       "LYRM9"       "NABP1"       "NBPF14"     
## [16] "NUAK2"       "NUDT4"       "RNASEH1-AS1" "SLC7A6"      "SPIDR"      
## [21] "STARD10"     "STK17A"      "ZFAS1"       "ZMAT1"       "ZNF84"

## [1] 30
##  [1] "ATAD1"    "CDC37L1"  "COG5"     "DIP2B"    "DSE"      "FCN1"    
##  [7] "HIVEP2"   "HOXB2"    "IGKV1-5"  "IL16"     "KLHL6"    "LRRC8D"  
## [13] "PARP16"   "PITPNC1"  "RAB37"    "RPS26"    "SIMC1"    "SLC25A33"
## [19] "SLC26A11" "FAM129A"  "GNPTAB"   "JAKMIP1"  "MT2A"     "SERTAD3" 
## [25] "SMPD2"

## [1] 31
##  [1] "LINC00623"   "POLD4"       "TRAV12-1"    "TRAV14DV4"   "WAPL"       
##  [6] "ZNF91"       "AC020915.3"  "C1orf162"    "CCL4"        "CD300A"     
## [11] "FCRL6"       "GPR65"       "HACD3"       "MESD"        "MFSD14A"    
## [16] "NNT-AS1"     "PARP11"      "S100A12"     "S1PR5"       "SMIM37"     
## [21] "THUMPD3-AS1" "TM2D1"       "TMEM138"     "TRBV6-1"     "TSPAN14"    
## [26] "TTC38"

## [1] 32
##  [1] "AC004687.1" "AC004854.2" "AC016405.3" "AC020911.2" "AC023157.3"
##  [6] "AC025164.1" "AC025171.3" "AC083880.1" "AC091271.1" "AC103591.3"
## [11] "AL121944.1" "AL139246.5" "AL357060.1" "AL451085.1" "ATP2B1-AS1"
## [16] "BX284668.6" "ID3"        "LINC01465"  "MATR3-1"    "MZF1-AS1"  
## [21] "NPIPB4"     "OSER1-DT"   "PARP8"      "SDR42E2"    "Z93241.1"

## [1] 33
##  [1] "IER3"      "PECR"      "PPP2R5C"   "ARHGAP10"  "C1orf21"   "CARD8-AS1"
##  [7] "CST7"      "DTX3L"     "GMFB"      "IGLV3-25"  "IRF9"      "MYO1F"    
## [13] "NKG7"      "ODF3B"     "PARP14"    "PARP9"     "PEX26"     "PLA2G16"  
## [19] "PPP2R5B"   "PTGDR"     "RSAD2"     "SLA"       "TNFRSF18"  "ZBP1"

## [1] 34
##  [1] "ABLIM1"    "ABTB1"     "ATP5MG"    "FBXO8"     "HDHD2"     "LIMD2"    
##  [7] "LINC00861" "LTB"       "MCUB"      "METAP1"    "NOP53"     "NT5DC1"   
## [13] "PCNP"      "RACK1"     "SGSM3"     "SMDT1"     "TBC1D10C"  "TBPL1"    
## [19] "TRAV9-2"   "CDK2AP2"   "FGR"       "NUS1"      "PARP4"     "S100A11"

## [1] 35
##  [1] "CSRNP1"  "GATA3"   "KANSL2"  "KDM6A"   "NR4A3"   "STK19"   "TOB2"   
##  [8] "ZNF490"  "ASCL2"   "BHLHE40" "CNOT4"   "GCN1"    "KANSL1"  "KMT2B"  
## [15] "KMT2C"   "PHF20"   "PHF20L1" "RECK"    "SH3BP5"  "SYNE1"   "TBX21"  
## [22] "TNFSF10"

## [1] 36
##  [1] "AC245297.3"  "ADA2"        "AL133415.1"  "C1GALT1"     "ERVK3-1"    
##  [6] "GIMAP6"      "GZMK"        "HEATR5B"     "KLF10"       "LEPROT"     
## [11] "OTULINL"     "SLC25A38"    "TOX"         "TRAV25"      "TRBV6-5"    
## [16] "BISPR"       "CRIP2"       "GAB3"        "MIR4435-2HG" "MX2"        
## [21] "MYBL1"       "MYO1G"       "SAMD9L"      "SPON2"       "SYNRG"

## [1] 37
##  [1] "CDC42SE2" "FAM118A"  "IER5"     "KLF12"    "MAP3K8"   "MTO1"    
##  [7] "PRKCH"    "RSRP1"    "SENP7"    "SLC12A7"  "TBC1D7"   "TCP11L2" 
## [13] "TMEM204"  "TTC31"    "UBL3"     "XRRA1"    "ZFAND5"   "ZNF831"  
## [19] "CAST"     "SAMD9"    "SDF2"     "TRIM22"   "XAF1"     "ZBTB8OS"

## [1] 38
##  [1] "CD82"    "FAM227B" "HIPK1"   "IL27RA"  "NEK1"    "PLK3"    "ST3GAL1"
##  [8] "BCL9L"   "DIAPH2"  "FNDC3B"  "GCA"     "GIMAP7"  "ITGAL"   "LCP1"   
## [15] "LY6E"    "PHF11"   "PHF23"   "RBSN"    "ROMO1"   "TYMP"

## [1] 39
##  [1] "COQ10A"     "SLC2A3"     "ZC3H12A"    "ZC3H12D"    "ZHX2"      
##  [6] "AC016831.7" "CCDC88B"    "CEMIP2"     "CRYBG1"     "CTBS"      
## [11] "DDIT4"      "FRY"        "GPRIN3"     "ICOS"       "KLF6"      
## [16] "LTBP3"      "NEAT1"      "NFKBIZ"     "PRDM2"      "RNF145"    
## [21] "RNMT"       "SLC9A8"     "TOB1"       "ZNF101"

## [1] 40
##  [1] "CLK4"    "EPB41"   "EVL"     "FLI1"    "LETMD1"  "MALAT1"  "NOSIP"  
##  [8] "POLL"    "RGS10"   "SEPT6"   "SH2D1A"  "SS18"    "STARD7"  "ZNF821" 
## [15] "ACAP2"   "ACAP3"   "AFF1"    "KMT2E"   "LRRFIP1" "MLLT10"  "PIM2"   
## [22] "PVT1"    "SELL"

for(n1 in names(goseq_res)){
  k = as.numeric(gsub("set_", "", n1))
  print(n1)
  print(gene_sets[[k]])
  print(goseq_res[[n1]])

}
## [1] "set_9"
##  [1] "ABHD5"     "ATG13"     "CD38"      "FCGR3A"    "LAX1"      "MMP24OS"  
##  [7] "ODF2L"     "PNPLA2"    "RASA2"     "RCSD1"     "SNRK"      "TESPA1"   
## [13] "TMC8"      "TRAV23DV6" "TRAV8-2"   "TUBD1"     "TUBE1"     "ZBTB25"   
## [19] "HSH2D"     "IFI44"     "IFI44L"    "OAS1"      "TRAT1"    
## $immune
##                                                                               category
## 5062                                     querec pbmc yf 17d vaccine age 18 45yo 3dy up
## 5063                                     querec pbmc yf 17d vaccine age 18 45yo 7dy up
## 2462 gse27241 ctrl vs digoxin treated rorgt ko cd4 tcell in th17 polarizing conditions
## 4972   howard t cell inact monov influenza a indonesia 05 2005 h5n1 age 18 49yo 1dy up
## 5102                              zak pbmc mrkad5 hiv 1 gag pol nef age 20 50yo 3dy up
## 1289                      gse17974 il4 and anti il12 vs untreated 24h act cd4 tcell dn
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 5062            7.573764e-06                0.9999998          5       27
## 5063            7.573764e-06                0.9999998          5       27
## 2462            8.505566e-05                0.9999971          4       22
## 4972            9.660053e-05                0.9999965          4       23
## 5102            1.058165e-04                0.9999937          5       45
## 1289            1.113896e-04                0.9999933          5       45
##             FDR
## 5062 0.01933582
## 5063 0.01933582
## 2462 0.09479256
## 4972 0.09479256
## 5102 0.09479256
## 1289 0.09479256
## 
## [1] "set_11"
##  [1] "BDH1"     "CCR6"     "CD48"     "LCLAT1"   "PTPRCAP"  "RNF139"  
##  [7] "SLC12A6"  "SLC25A25" "TRAM1"    "ATP8B2"   "CD2"      "CD58"    
## [13] "CMTM6"    "GIMAP4"   "HM13"     "LPCAT3"   "LPCAT4"   "LPGAT1"  
## [19] "SLC12A9" 
## $reactome
##                             category over_represented_pvalue
## 398 glycerophospholipid biosynthesis            2.354282e-05
## 721          phospholipid metabolism            1.799579e-04
## 31      acyl chain remodelling of pe            4.096445e-04
## 34      acyl chain remodelling of ps            4.096445e-04
## 32      acyl chain remodelling of pg            4.097818e-04
##     under_represented_pvalue numDEInCat numInCat        FDR
## 398                0.9999995          4       16 0.02827492
## 721                0.9999928          4       26 0.09842958
## 31                 0.9999986          2        3 0.09842958
## 34                 0.9999986          2        3 0.09842958
## 32                 0.9999986          2        3 0.09842958
## 
## $go_bp
##                                            category over_represented_pvalue
## 2409 phosphatidylethanolamine acyl chain remodeling            3.028192e-06
## 2412         phosphatidylglycerol metabolic process            7.512040e-06
##      under_represented_pvalue numDEInCat numInCat        FDR
## 2409                        1          3        4 0.01448384
## 2412                        1          3        5 0.01796504
## 
## $immune
##                                                  category
## 1106                  gse17721 lps vs pam3csk4 1h bmdc up
## 3991 gse41867 memory vs exhausted cd8 tcell day30 lcmv dn
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1106            3.056575e-05                0.9999992          4       20
## 3991            3.718477e-05                0.9999983          5       42
##             FDR
## 1106 0.09493271
## 3991 0.09493271
## 
## [1] "set_18"
##  [1] "CD28"    "DBP"     "PECAM1"  "BATF"    "CD320"   "CISH"    "CMIP"   
##  [8] "FBXO9"   "G2E3"    "IFI35"   "IL2RB"   "IL2RG"   "IL32"    "INPP5D" 
## [15] "MYOM2"   "NQO2"    "P4HTM"   "RAPGEF1" "SLC35A2" "TIPARP"  "UGCG"   
## [22] "ZNF276"  "ZNF708" 
## $reactome
##                                             category over_represented_pvalue
## 491 interleukin 3 interleukin 5 and gm csf signaling            8.564168e-06
## 498               interleukin receptor shc signaling            5.799668e-05
## 995                        signaling by interleukins            6.607657e-05
## 486                   interleukin 2 family signaling            2.608409e-04
##     under_represented_pvalue numDEInCat numInCat        FDR
## 491                0.9999999          4       12 0.01028557
## 498                0.9999994          3        7 0.02645265
## 995                0.9999946          7       92 0.02645265
## 486                0.9999946          3       11 0.07831747
## 
## [1] "set_21"
##  [1] "ADPRHL2"    "BTN3A1"     "LTA4H"      "PITPNA-AS1" "TMEM245"   
##  [6] "UTP6"       "ALOX5AP"    "APOL1"      "APOL6"      "BTN3A2"    
## [11] "BUD23"      "CTSW"       "ECPAS"      "GBP1"       "GBP3"      
## [16] "GBP5"       "GZMM"       "HEXDC"      "MCTP2"      "NCBP3"     
## [21] "PEX11B"     "SP140"      "TAOK3"      "TGFBR3"     "TMEM62"    
## $go_bp
##                                                   category
## 693 disruption of anatomical structure in another organism
##     over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 693            6.700668e-07                        1          5       17
##             FDR
## 693 0.003204929
## 
## $immune
##                                                                               category
## 892                           gse1740 mcsf vs mcsf and ifng day2 derived macrophage up
## 2497                         gse2770 il12 and tgfb vs il4 treated act cd4 tcell 48h dn
## 895                       gse1740 unstim vs ifna stimulated mcsf derived macrophage dn
## 4959   howard b cell inact monov influenza a indonesia 05 2005 h5n1 age 18 49yo 1dy up
## 5035             nakaya pbmc imuvac male age 14 27yo 1d postboost vs 0dy preimm tiv up
## 509                                                gse1432 1h vs 24h ifng microglia dn
## 4963 howard monocyte inact monov influenza a indonesia 05 2005 h5n1 age 18 49yo 1dy up
## 152                             gse1112 hy cd8ab vs hy cd8aa thymocyte rtoc culture up
## 4966 howard neutrophil inact monov influenza a indonesia 05 2005 h5n1 age 18 49yo 3dy 
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 892             1.905730e-06                0.9999999          6       32
## 2497            7.532723e-06                0.9999996          6       40
## 895             1.530649e-05                0.9999991          6       45
## 4959            6.683699e-05                0.9999992          3        7
## 5035            6.685649e-05                0.9999992          3        7
## 509             7.497802e-05                0.9999942          6       59
## 4963            1.194293e-04                0.9999899          6       64
## 152             1.368987e-04                0.9999913          5       41
## 4966            1.540312e-04                0.9999899          5       42
##              FDR
## 892  0.009730658
## 2497 0.019231041
## 895  0.026051649
## 4959 0.063806293
## 5035 0.063806293
## 509  0.063806293
## 4963 0.087115163
## 152  0.087375595
## 4966 0.087387036
## 
## [1] "set_24"
##  [1] "COL18A1"   "DALRD3"    "NECAP2"    "ADGRG1"    "ARHGEF3"   "ARL4C"    
##  [7] "COL6A3"    "COLGALT1"  "CX3CR1"    "FGFBP2"    "LAIR2"     "LINC01871"
## [13] "LPIN1"     "LPIN2"     "LY96"      "PCED1B"    "PLEK"      "RAP1GAP2" 
## [19] "RNPEPL1"   "SP140L"    "TCAF2"     "TTC16"     "VPS13D"    "ZNF683"   
## $reactome
##                                         category over_represented_pvalue
## 167  collagen biosynthesis and modifying enzymes            2.263001e-05
## 170                           collagen formation            8.391148e-05
## 168                 collagen chain trimerization            1.166352e-04
## 1170                   triglyceride biosynthesis            1.197099e-04
## 1073                             synthesis of pe            3.589348e-04
##      under_represented_pvalue numDEInCat numInCat        FDR
## 167                 0.9999998          3        6 0.02717864
## 170                 0.9999989          3        9 0.03594291
## 168                 1.0000000          2        2 0.03594291
## 1170                1.0000000          2        2 0.03594291
## 1073                0.9999988          2        3 0.08621613
## 
## [1] "set_25"
##  [1] "C6orf62" "CCNH"    "COQ10B"  "DGKA"    "ERCC5"   "FHIT"    "INPP4B" 
##  [8] "KLHL24"  "LEF1"    "MYNN"    "NFYB"    "TCF7"    "TPP2"    "ACAP1"  
## [15] "CREBZF"  "ETNK1"   "NARF"    "NFE2L1"  "PPRC1"   "RHOH"    "STAT4"  
## [22] "TGS1"    "VPS36"   "XBP1"   
## $immune
##                                        category over_represented_pvalue
## 2996 gse32901 th1 vs th17 enriched cd4 tcell up            1.917639e-05
##      under_represented_pvalue numDEInCat numInCat        FDR
## 2996                0.9999989          6       49 0.09791465
## 
## [1] "set_27"
##  [1] "CBR3"     "DPEP2"    "GGT7"     "LIMS1"    "NEU1"     "SERTAD2" 
##  [7] "SLC25A32" "USP3"     "ZNF677"   "B3GALT4"  "FKBP11"   "FUT11"   
## [13] "GALNS"    "GZMB"     "PARVG"    "PLAA"     "RSU1"     "SACS"    
## [19] "SH3BGRL3" "SRGN"     "ST6GAL1"  "TRIB2"   
## $reactome
##                                    category over_represented_pvalue
## 105        blood group systems biosynthesis            0.0001173633
## 42  aflatoxin activation and detoxification            0.0001262795
## 101                   biological oxidations            0.0001807014
##     under_represented_pvalue numDEInCat numInCat        FDR
## 105                1.0000000          2        2 0.07234081
## 42                 1.0000000          2        2 0.07234081
## 101                0.9999968          3       11 0.07234081
## 
## [1] "set_33"
##  [1] "IER3"      "PECR"      "PPP2R5C"   "ARHGAP10"  "C1orf21"   "CARD8-AS1"
##  [7] "CST7"      "DTX3L"     "GMFB"      "IGLV3-25"  "IRF9"      "MYO1F"    
## [13] "NKG7"      "ODF3B"     "PARP14"    "PARP9"     "PEX26"     "PLA2G16"  
## [19] "PPP2R5B"   "PTGDR"     "RSAD2"     "SLA"       "TNFRSF18"  "ZBP1"     
## $immune
##                                                                               category
## 1456     gse19888 adenosine a3r inh vs act with inhibitor pretreatment in mast cell up
## 1460                    gse19888 adenosine a3r inh vs tcell membranes act mast cell up
## 3886                       gse40666 untreated vs ifna stim stat1 ko cd8 tcell 90min up
## 4432               gse5589 lps and il10 vs lps and il6 stim il6 ko macrophage 45min up
## 3962              gse41867 day15 effector vs day30 exhausted cd8 tcell lcmv clone13 up
## 379                                        gse13485 ctrl vs day7 yf17d vaccine pbmc dn
## 4965 howard neutrophil inact monov influenza a indonesia 05 2005 h5n1 age 18 49yo 1dy 
## 2412                                   gse26890 cxcr1 neg vs pos effector cd8 tcell up
## 2348                                    gse26030 th1 vs th17 day5 post polarization up
## 3275                                                 gse36078 wt vs il1r ko lung dc dn
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1456            1.598740e-06                0.9999999          7       49
## 1460            2.692155e-06                0.9999999          7       53
## 3886            3.504527e-06                0.9999999          6       35
## 4432            5.367951e-06                0.9999997          7       59
## 3962            1.159691e-05                0.9999994          6       47
## 379             1.540305e-05                0.9999989          7       68
## 4965            2.016917e-05                0.9999981          8      104
## 2412            3.365894e-05                0.9999978          6       53
## 2348            4.030853e-05                0.9999973          6       52
## 3275            4.338874e-05                0.9999979          5       36
##              FDR
## 1456 0.005964705
## 1460 0.005964705
## 3886 0.005964705
## 4432 0.006852189
## 3962 0.011842768
## 379  0.013107997
## 4965 0.014711966
## 2412 0.021182552
## 2348 0.021182552
## 3275 0.021182552
## 
## [1] "set_35"
##  [1] "CSRNP1"  "GATA3"   "KANSL2"  "KDM6A"   "NR4A3"   "STK19"   "TOB2"   
##  [8] "ZNF490"  "ASCL2"   "BHLHE40" "CNOT4"   "GCN1"    "KANSL1"  "KMT2B"  
## [15] "KMT2C"   "PHF20"   "PHF20L1" "RECK"    "SH3BP5"  "SYNE1"   "TBX21"  
## [22] "TNFSF10"
## $reactome
##                                                     category
## 352 formation of wdr5 containing histone modifying complexes
## 295                 epigenetic regulation of gene expression
## 153                              chromatin modifying enzymes
##     over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 352            1.711024e-10                1.0000000          7       16
## 295            5.818645e-08                1.0000000          7       38
## 153            4.107397e-05                0.9999975          6       61
##              FDR
## 352 2.054940e-07
## 295 3.494096e-05
## 153 1.644328e-02
## 
## $go_bp
##                                                               category
## 1115                                              histone modification
## 1112                                         histone h3 k4 methylation
## 1114                                               histone methylation
## 2369                                       peptidyl lysine methylation
## 2689                        positive regulation of histone methylation
## 3476 regulation of dosage compensation by inactivation of x chromosome
## 3580                           regulation of histone h3 k4 methylation
## 3147                                               protein methylation
## 3581                                 regulation of histone methylation
## 1113                                            histone h4 acetylation
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1115            7.962431e-07                1.0000000          6       29
## 1112            2.131837e-06                1.0000000          4        8
## 1114            3.822025e-06                1.0000000          4       10
## 2369            1.022126e-05                0.9999998          4       12
## 2689            1.771221e-05                0.9999999          3        5
## 3476            1.771221e-05                0.9999999          3        5
## 3580            1.771221e-05                0.9999999          3        5
## 3147            3.004498e-05                0.9999993          4       15
## 3581            3.708037e-05                0.9999997          3        7
## 1113            6.288136e-05                1.0000000          2        2
##              FDR
## 1115 0.003808431
## 1112 0.005098289
## 1114 0.006093582
## 2369 0.012102503
## 2689 0.012102503
## 3476 0.012102503
## 3580 0.012102503
## 3147 0.017963144
## 3581 0.019706158
## 1113 0.030076153
## 
## [1] "set_36"
##  [1] "AC245297.3"  "ADA2"        "AL133415.1"  "C1GALT1"     "ERVK3-1"    
##  [6] "GIMAP6"      "GZMK"        "HEATR5B"     "KLF10"       "LEPROT"     
## [11] "OTULINL"     "SLC25A38"    "TOX"         "TRAV25"      "TRBV6-5"    
## [16] "BISPR"       "CRIP2"       "GAB3"        "MIR4435-2HG" "MX2"        
## [21] "MYBL1"       "MYO1G"       "SAMD9L"      "SPON2"       "SYNRG"      
## $reactome
##                                                 category
## 239 diseases associated with o glycosylation of proteins
## 682                               o linked glycosylation
##     over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 239            6.447454e-05                0.9999999          2        3
## 682            1.245271e-04                0.9999997          2        4
##            FDR
## 239 0.07477851
## 682 0.07477851
saveRDS(goseq_res, sprintf("output/gene_set_enrichments_%s.RDS", 
                           file_tag))

Session information

gc()
##            used  (Mb) gc trigger  (Mb) limit (Mb) max used  (Mb)
## Ncells  8958389 478.5   16391124 875.4         NA 16391124 875.4
## Vcells 19173826 146.3   60252964 459.7      65536 77218972 589.2
sessionInfo()
## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] TxDb.Hsapiens.UCSC.hg38.knownGene_3.16.0
##  [2] GenomicFeatures_1.50.4                  
##  [3] GenomicRanges_1.50.2                    
##  [4] GenomeInfoDb_1.34.9                     
##  [5] org.Hs.eg.db_3.16.0                     
##  [6] AnnotationDbi_1.60.2                    
##  [7] IRanges_2.32.0                          
##  [8] S4Vectors_0.36.2                        
##  [9] Biobase_2.58.0                          
## [10] BiocGenerics_0.44.0                     
## [11] goseq_1.50.0                            
## [12] geneLenDataBase_1.34.0                  
## [13] BiasedUrn_2.0.10                        
## [14] fgsea_1.24.0                            
## [15] biomaRt_2.54.1                          
## [16] limma_3.54.2                            
## [17] tidyr_1.3.0                             
## [18] ggpubr_0.6.0                            
## [19] ggplot2_3.4.2                           
## [20] data.table_1.14.8                       
## 
## loaded via a namespace (and not attached):
##  [1] nlme_3.1-162                matrixStats_1.0.0          
##  [3] bitops_1.0-7                bit64_4.0.5                
##  [5] filelock_1.0.2              progress_1.2.2             
##  [7] httr_1.4.6                  tools_4.2.3                
##  [9] backports_1.4.1             bslib_0.4.2                
## [11] utf8_1.2.3                  R6_2.5.1                   
## [13] mgcv_1.8-42                 DBI_1.1.3                  
## [15] colorspace_2.1-0            withr_2.5.0                
## [17] tidyselect_1.2.0            prettyunits_1.1.1          
## [19] bit_4.0.5                   curl_5.0.1                 
## [21] compiler_4.2.3              cli_3.6.1                  
## [23] xml2_1.3.4                  DelayedArray_0.24.0        
## [25] rtracklayer_1.58.0          sass_0.4.5                 
## [27] scales_1.2.1                rappdirs_0.3.3             
## [29] Rsamtools_2.14.0            stringr_1.5.0              
## [31] digest_0.6.31               rmarkdown_2.21             
## [33] XVector_0.38.0              pkgconfig_2.0.3            
## [35] htmltools_0.5.5             MatrixGenerics_1.10.0      
## [37] dbplyr_2.3.2                fastmap_1.1.1              
## [39] rlang_1.1.0                 rstudioapi_0.14            
## [41] RSQLite_2.3.1               BiocIO_1.8.0               
## [43] jquerylib_0.1.4             generics_0.1.3             
## [45] jsonlite_1.8.4              BiocParallel_1.32.6        
## [47] dplyr_1.1.2                 car_3.1-2                  
## [49] RCurl_1.98-1.12             magrittr_2.0.3             
## [51] GO.db_3.16.0                GenomeInfoDbData_1.2.9     
## [53] Matrix_1.6-4                Rcpp_1.0.10                
## [55] munsell_0.5.0               fansi_1.0.4                
## [57] abind_1.4-5                 lifecycle_1.0.3            
## [59] stringi_1.7.12              yaml_2.3.7                 
## [61] carData_3.0-5               SummarizedExperiment_1.28.0
## [63] zlibbioc_1.44.0             BiocFileCache_2.6.1        
## [65] grid_4.2.3                  blob_1.2.4                 
## [67] parallel_4.2.3              crayon_1.5.2               
## [69] lattice_0.20-45             splines_4.2.3              
## [71] Biostrings_2.66.0           cowplot_1.1.1              
## [73] hms_1.1.3                   KEGGREST_1.38.0            
## [75] knitr_1.44                  pillar_1.9.0               
## [77] rjson_0.2.21                ggsignif_0.6.4             
## [79] codetools_0.2-19            fastmatch_1.1-3            
## [81] XML_3.99-0.14               glue_1.6.2                 
## [83] evaluate_0.20               png_0.1-8                  
## [85] vctrs_0.6.2                 gtable_0.3.3               
## [87] purrr_1.0.1                 cachem_1.0.7               
## [89] xfun_0.39                   broom_1.0.4                
## [91] restfulr_0.0.15             rstatix_0.7.2              
## [93] tibble_3.2.1                GenomicAlignments_1.34.1   
## [95] memoise_2.0.1